I chiseled mine out and put the flange over it. I tried a flange that fits inside the waste pipe but the flange from the toliet wouldn't set inside. I cut part of the flange off so I didn't have to go as deep into the concrete. I drilled holes for lead anchors before I glued on the flange, then glued flange and used stainless screws into the anchors.

The flange should be flush with the finished floor. Use a punch on the tile to mark the drilling point so your drill will not skate. Use a masonary bit. Drill a little then hit the puch again from time to time to help get some bit as the tile is very tough.

Dry fit flange and place toliet on flange before gluing to make sure your have some clearence!!!!